Naruto The Ultimate Shinobi
by anime-death-angel
Summary: After being thrown out on the streets and left for dead by a mob attack at age four Danzo has his ROOT abduct Naruto where he is injected with DNA of the strongest ninja to ever live. Based off Challenger's Naruto Ultimate Shinobi Challenge. Mult. Bloodline Naruto. NarutoxHarem
1. Chapter 1

**ROOT Base Laboratory**

In a dark and barely lit lab was a tank contained with a green liquid. In it was a small figure that was 10 years old and naked. Over his mouth was what looked like a breathing apparatus and tubes were connected to certain parts of his body. He was Naruto Uzumaki Namikaze, the son of the **Kiiroi Senkou** and **Akai Chishio no Habanero**, Minato Namikaze and Kushina Uzumaki.

When Naruto was four, he was kicked out of the orphanage and beaten on his birthday. Before the Anbu could take him to the hospital, Danzo had his ROOT forces abduct the boy from the alley and brought him underground to ROOT HQ. So for the next six years, he had his ROOT teach Naruto the shinobi basics and had the medics and scientists perform experiments on the boy and inject the DNA of the strongest Kage from four of the five great shinobi crounties.

The DNA of Madara Uchiha, Hashirama Senju, the Nidaime and Sandaime Tsuchikage Mu and Onoki, the Nidaime Mikukage and the Sandaime and Yondaime Kazekage were injected into his body by melding their latent abilities or bloodline traits into a single body. Danzo also abducted an entire Uchiha family and had Fu use his **Mind Body Switch Technique** on the two sons to force them to butcher their parents and sister to death, which awaken their Mangekyo Sharingan. Afterward Danzo had the two brothers killed and implanted their eyes into Naruto's which granted him the **Eternal Mangekyo Sharingan** which adapted to Madara's DNA.

Danzo Shimura, the war hawk who competed with Hiruzen for the title of Sandaime, watched with look of glee in his single left eye. A dark smile was on his face as he watched the boy's unconscious form float in the tank. _'Sarutobi you fool. You have given me the ultimate weapon and with him under my command, I'll overthrow you and create Konoha in my image. With the abilities of the greatest ninja to ever exist and the powers of the Kyuubi no Yoko in his being, I will be unstoppable. The Shinobi world will be mine to rule.' _He thought and would have ranted on in his mind until an alarm went off and several explosions were heard.

"What was that!?" He yelled as a ROOT Member appeared kneeling before Danzo.

"Danzo-sama. We have been breached. The Sandaime and his ANBU forces have surrounded the hidden base and right now his men have entered." He explains and the war hawks eye widens in horror.

"What!? How did he find the base!?" He demanded as another explosion echoed in the base.

"W-we don't know Danzo-sama." The ROOT ANBU answered while the man grits his teeth and squeezes his cane.

**Earlier**

Outside Danzo's compound, Hiruzen Sarutobi, the **Shinobi no Kami**, and **Sandaime Hokage** of Konoha was currently in his battle armor with a platoon of his best ANBU surrounding the compound. His double agent, Neko had sent the man a message that she had found Naruto in the hidden base that was under Danzo's compound.

To say Sarutobi was pissed was an understatement. He was going to kill that fool for what he's done. He already had a few of his men set explosives on key points of the compound and they dealt with the ROOT guards. That was when an ANBU with an Inu mask and gravity defying silver hair appeared, kneeling before his leader.

"Hokage-sama, the compound is completely surrounded and we have dealt with the guards." He says and the man nods.

"Good, have your unit along with Tori and Taka get ready to enter once the explosives are set off." He says.

"Hai!" Inu says and shunshins away. Sarutobi bites his thumb and performs a few hand seals.

"**Kuchiyose no Jutsu**." He says and in a puff of smoke, a monkey with wild white hair and brown yellow eyes appears. He was the monkey king, Enma.

"**Sarutobi? Why have you summoned me?" **He asks.

"Enma I need your help in dealing with a bothersome fly. He's actually an old associate named Danzo." He says.

Enma's eyes widen but the return to normal. **"So that war hawk is up to his old tricks again? Very well, I will help you deal with that fool. Hopefully I'll get to break his other arm." **He says with a chuckle. **"Henge." **Enma transforms into an Adamantine Staff that was black with gold tips on the end. Sarutobi then looks at Tori.

"Do it." He says. Tori nods and lights up a flare and 15 more light up from different locations and then does a ram seal.

"Katsu." He mutters and an explosion from the first gate is seen. Then a few more explosions are heard.

"Go!" Sarutobi says, and that was when ANBU leaped from the trees, passing Sarutobi, and heading towards the compound as do the other black ops. Sarutobi twirls the staff in his hands and leaps out of the trees to join in the battle.

**Currently**

Danzo was pissed. No, he was beyond pissed. He kept wondering how that old fool found his base. ROOT ANBU were running left and right and the sounds of explosions, blades clashing, and screaming was heard. Another one of his ROOT ANBU appeared.

"Danzo-sama, half of our forces have been killed or captured. We must retreat to one of our bases." He says.

Danzo growls in frustration as he gazes at his soon to be weapon in the tank. "No, I am not leaving without my weapon!" He says and the Ne member looks at him in shock.

"D-Danzo-sama we are being overwhelmed. Almost all of the escape routes have been destroyed or blocked. We must escape now!" The ROOT ANBU reasoned. Danzo snarles and slams the tip of his cane on the floor, creating a small crack.

"Damn you… damn you Hiruzen Sarutobi! Let's go!" He says and takes one last glance at the sleeping Naruto and frowns before heading into a hidden escape route. Meanwhile, Sarutobi swatted away a tanto that was aimed at his head by a ROOT soldier and then strikes the drone on the side of his head and a sickening crunch was heard as he fell to the floor with blood oozing out of his head.

He then throws a volley of shuriken at a few and performs a few hand seals. **"Kage Shuriken Bushin no Jutsu." **He says and the five shuriken become 15 and hit three of the distracted ROOT who were dodging some of the attacks the ANBU pulled and fell to the ground dead.

"**Chidori!" **The Inu masked ANBU yelled out as he cut through the ROOT leaving a lightning streak as he ran by the smoking and electrocuted bodies of the drones he killed.

Inu sees a door that had the kanji lab on it and kicks the door to the lab down, surprising the med and scientists. A group of ANBU leap passed him and restrained the medics and scientist that tried to escape. Inu looks around and notices a green tank. He walks towards it and gasps when he sees a blonde ten year old floating in it with a breathing apparatus covering half of his face and tubes were on certain parts of his body.

"It's him." He says and walks over to a restrained scientist and picks him up by his collar. "You, how do we get him out of that tank?" he demand and the scientist just scoffs at Inu. Inu then pulls a kunai out and stabs him in the shoulder, making him scream out in pain. "The next one will end up in your skull." He says as he pushes the kunai even further into the man's shoulder, making a bloodstain appear and squirt out.

"How do we get him out?" He demands in a dark tone. The scientist looks up and speaks.

"I-it's the blue button." He says only to be knocked out by the man.

"Get this scum and the others out of here and send them to Ibiki. He hasn't had any decent playmates for awhile." He says and the ANBU drag the kicking and screaming scientists out of the lab.

"Neko with me." He says and she nods as they walk towards the tank. "Check for traps." He commands.

"Hai Sempai." She says and checks the tank for any traps. "No traps Sempai." She says and he nods and pushes the blue button. The green liquid bubbles up and starts to drain away until it was empty with the unconscious blonde boy hanging from the tubes. The tank moves down and the boy's body starts to fall out but Neko catches his sleeping form.

She carefully removes the tubes and breathing apparatus and sets him down gently. She then grabs one of the lab coats and wraps it around his body to keep him warm. Inu was currently holding the side of his mask and static was heard. He then moves his hand down and looks at Neko.

"Neko I am going to join up with Hokage-sama and help him hunt down Danzo. I'm leaving you in charge with the squad. Make sure nothing happens to the boy." He says and she salutes him while he shunshins away.

**Outside the compound**

Danzo and four of his ROOT were heading for the south gate until a barrage of kunai stopped them in their track. Danzo curses as 20 ANBU appear and surround him. "Do you honestly think I'd let you escape after what you have done Danzo?" Said a deep and harsh voice. The war hawk turns around to see a pissed off Hiruzen glaring at the man with his Adamant Staff in his hand.

"Hokage-_sama_ to what do I owe the honor?" He asks in a mocking voice.

"Silence you traitor. What you have done is unforgivable and considered an act of treason. I know you had help from certain members of the council and I will find out who they were. Give up. Your forces are defeated, the village is on complete lockdown and I already have my Jonin tracking down your other bases." He states as he releases his KI on the man.

Danzo grits his teeth and glares at Hiruzen. "You were a fool to not let that boy be a weapon. I did what was necessary to make sure this village remained as the strongest. Why the Nidaime let a weak fool like you become Hokage I'll never know." He said and that only pissed Hiruzen off further.

"I suggest you pick your next words carefully Danzo. You have nowhere to run or hide. You did not become Hokage back then and you will not become it now. Not as long as I draw breath from my body." He says. One of the ROOT tried to charge at Hiruzen with a kunai only to be decapitated and stabbed by three ANBU. The other three were killed by a volley of kunai and shuriken and fall over dead.

Danzo's eyes widen as he saw his last line of defense perish. He then pulls out the hidden blade in his cane and charges at Hiruzen. The god of Shinobi swats the blade away with his staff, making Danzo's eye widen in shock. Before the man could react, Sarutobi struck him in the kneecap, and the sound of bones snapping from his leg was heard. Danzo cries out in pain and collapses.

He then reaches for the blade and tries to grab it, but Hiruzen slams his foot on the man's hand, crushing it. "You never did know when to quit Danzo." He says and adds more pressure on his foot and hears the man's knuckles crack and break, making his hand useless. Danzo looks up at Sarutobi with a look of hate in his eyes.

"I may die Hiruzen but as long as you hold on to your stupid beliefs of peace in the ninja world, Konoha will always be weak. That boy will bring our village to the top of the elementals." He stated. Sarutobi grabbed the man by his hair and pulled him up to his eye level.

"Yes he will but it won't be through your envision." He says and buries his fist into the man's gut making him hunch over and then backhands him in the temple, knocking him out.

That was when Inu appears knelling before the Hokage. "Did your squad recover the boy Inu?" Sarutobi asks and the ANBU captain nods. "Good. Have Danzo sent to Ibiki and tell him to show no mercy." He ordered and Inu nods as he grabs Danzo and shunshins away.

"Show no mercy? Damn. I almost fell sorry for the poor bastard." Tora says as some of the other ANBU nod. A smirk appears on Sarutobi's face when he heard the comment but then spoke up.

"Alright then, the rest of you make there are no stragglers and place a restriction sign around the compound. Tora inform the ANBU commander that the lockdown is over." He says and the ANBU nods and shunshins away.

That was when Neko appears with the blond haired boy wrapped in a lab coat. "Here's the boy Hokage-sama. The squads have managed to kill most of the ROOT ANBU and the ones that survived are being detained." She says. Sarutobi nods. "Good work Neko. You and Shishi (lion) come with me to the hospital, Jackal!" He called out and an ANBU wearing a Jackal mask appeared. "I need you and two squads of ANBU try to find Jiraiya and Tsunade and tell them it is urgent." He says getting a nod from jackal and shunshins away.

Sarutobi looks at the sleeping form of Naruto and his gaze softens. "I don't know what that man has done to you my boy but I promise he will pay." He says and the three head to the hospital. Hiruzen was currently sitting beside the bed the sleeping boy was in. Naruto still had his blond spiky hair but it was longer (Madara in his youth). His whisker marks were faded and he had canines jutting from his upper lip.

Neko and Shishi (lion) were guarding the door outside. That was when a white blur shot through the window shocking Sarutobi and the two ANBU bust through the door with their hands on the hilts of their Ninjatos. They then realized that the panting man was none other than Jiraiya, the Gama Sennin.

"S-sensei I got her as fast as I could and Tsunade is currently on her way he-GAAHHH!" He says as a female with long platinum blonde hair that was tied in two loose ponytails wearing a grey, kimono-style blouse with no sleeves which revealed her impressive cleavage with blue pants, open toed heels, and a green jacket with the kanji for gamble on it came through the window and landed on Jiraiya's spine panting heavily.

"Where is he Sen-mmmph?!" She started to yell but Sarutobi covered her mouth doing a shushing motion with his finger.

"Oh Kami my spine." Jiraiya groaned out laying across the ground face first while the ANBU sweat drop at the scene.

Sarutobi removes his hand from her mouth and gives her a stern look. "Use your inside voice Tsunade and please get off of Jiraiya. You're standing on his spine." He informed her and she looks down at her perverted teammate.

"Oh sorry about that pervert." She hops off the groaning man who then got up and popped his back in place.

"Man that hurt." He says and then turns his head to Naruto's sleeping form and his eyes widen. "Sensei is that" Jiraiya asks and Sarutobi nods.

"I'm glad you both are here. Jiraiya I need you to check his body for any odd seals and to check _that_ one." He emphasizes. Jiraiya blinks but nods.

After checking the boy's body for any odd seals, he looks at the Shiki Fuin and blinks for a while. "That's odd. The seal is intact and hasn't been tampered with but for some reason it looks like its formation has been rotated or reversed. Sensei what the hell is up with this?" He asks. Sarutobi was about to speak up until the head doctor walked in.

"Excuse me for the interruption Hokage-sama but I am finished analyzing the blood and DNA samples." He says.

"I see. Can you tell me is there any odd changes Nishiki-san?" He asks and Tsunade blinks at this wondering why he would do that. Nishiki tilts his glasses up and sighs.

"What I'm about to tell you will shock you, especially you Tsunade-sama." He says and they raise an eyebrow.

"What does his condition have to do with us or sensei?" Jiraiya asks. "You're not gonna believe this but after doing some careful analyzing of the samples and matching them… I found out that the boy carries the DNA of two individuals in this village and the rest foreign. Tsunade-sama… your grandfathers DNA and blood types match the boys." He said. Hiruzen's eyes bulge out of his head and his jaw drops, Jiraiya fainted, and Tsunade was gapping like a fish.

"Please tell me that this is a joke Nishiki-san." He asks and the man shakes his head.

"No. He also carries the DNA of Madara Uchiha, Hashirama Senju, the Nidaime and Sandaime Tsuchikage Mu and Onoki, the Nidaime Mikukage Kuromizu of the Hozuki clan and the Sandaime and Yondaime Kazekage " Ha finished.

"HE WHAT!?" Hiruzen yells and the entire room shakes. Shizune and Tonton were panting as they finally made it to the hospital until they heard the yell.

"What was that?" She wondered and Tonton just oinked.

**Morning**

Hiruzen couldn't believe what he heard the other day. Naruto Uzumaki Namikaze was injected with the DNA of not only the strongest Hokage and Uchiha to ever live, but he also the DNA of some of the strongest Kages and has possibly inheriting their bloodlines and latent abilities. "This is so troublesome. I can't believe Danzo did this to him." He mumbles.

Tsunade walks in the waiting room yawning and rubbing her eyes. "Hey Sensei, you look like you've been through hell and back." She jokes and he chuckles at her comment.

"I really need to find a successor and soon. I'm really getting too old for this. The council is going to be a pain today." He mumbles. "Anyway you did a physical on the boy. Is he still asleep?" He asks

She nods and frowns. "Yes. Danzo had his medics put a powerful sleeping drug into the boy's body. It only lasts for a day so he should wake up in three hours. As for his physical, aside from the slight muscle on his body and incisors in his upper jaw being longer than normal, he's fine but the real question is how in the hell Danzo acquired those DNA samples most of them were top secret and some of them are foreign?" She wondered with a serious expression on her face. "But that's not what's got me worried. He shouldn't have survived the process of having different forms and structures of DNA into his body. It should've killed him since his blood and DNA type didn't even match half of them. I mean when we found out about how Orochimaru tried to replicate the Mokuton my grandfather had with those 60 babies, only one survived the process." She explained and he nods.

"It must've been the Kyubi's doing. That's the only explanation I can come up with Tsunade." Sarutobi states and she sighs.

"Question is how in the hell did Danzo get his hands on the boy?" She asks. That was when Jiraiya walked out the door wiping a bead of sweat off of his forehead.

"I'd like to know as well Sensei. You said Minato's kid would be safe in your hands and away from Danzo so spill it." He said in a tone that meant he wasn't joking. The reason he couldn't visit Naruto so much was because he had to update his spy network that was spread across the elementals. He did however send the kid gifts and small sums of money to Hiruzen for Naruto.

But when he was sent that message about how his sensei and several ANBU squads found the boy in his underground basement, he moved at speeds that would make Gai and his late student green with envy and look like a joke. Tsunade did the same since Sarutobi only contacted her when the situation was dire.

Hiruzen rubs the bridge of his nose and speaks up. "It happened six years ago. The matron of the orphanage kicked Naruto out and left him to fend for himself in the street, afterward a group of civilians cornered the boy in an alley and beat him. I was in a council meeting when it happen, my Anbu manage to detain the mob and I sent them all to Ibiki but I couldn't find Naruto anywhere. I had one of my ANBU play as a double agent in his so called 'disbanded' organization for 6 years and when I got the message of a blonde boy being experimented on I placed the village on lockdown and I along with my best ANBU stormed his compound." He explains.

That was when Jiraiya clenched his fists in anger and he was releasing a small amount of KI in the hospital. "I'm gonna kill that crippled bastard." He snarled and slammed his fist into a wall, leaving a small crack in it.

"Please tell me you're gonna execute that bastard. Because if you don't I will." Tsunade said as she cracked her knuckles.

Sarutobi has a grim look on his face. "Oh don't worry I plan on executing him. He's now under the care of Ibiki and Inoichi. I know that certain members on the council are in league with them and they too will pay the ultimate price." He says. That was when Jiraiya spoke. "So let me get this straight old man. Naruto not only has the DNA of the most powerful Senju and Uchiha in history but he also has the DNA of 5 foreign Kage in him as well?" He asks and Sarutobi nods.

"So it's possible that he has inherited the abilities of said people like the Sharingan and the Shodaime's Mokuton and let's not forget about the Nidaime Mizukage's water abilities of the Hozuki clan, the Jiton of the San and Yondaime Kazekage and the Jinton and flight techniques that have been passed down from Tsuchikage to Tsuchikage." He says and Tsunade's eyes widen.

"But there's a slim chance that he can even have the Mokuton since no other person in my clan other than my grandfather had the bloodline other than that ANBU but his form of Mokuton is weaker and it doesn't have the properties of the one my grandpa had." She stated.

"But with the Kyubi sealed in the boy its possible Tsunade." Jiraiya says. "But let's not forget about the DNA of the Nidaime Tsuchikage Mu whose mastery of the **Meisaigakure no Jutsu**(Hiding with Camouflage Technique) was so powerful that he earned the name **Mujin**(non-person) where even the most skilled Sensor types couldn't detect him.

"Remember that the Sandaime Kazekage Jiton(magnet Release) could also manifest in the boy, combined with the Yondaime Jiton the boy's mastery over the element could be greater than the two combined." Sarutobi says as he rubs his chin in thought and looks at Jiraiya. "Jiraiya I want you to go to Danzo's main office in his compound and find out any secrets Danzo has kept hidden. His notes and journals should still be there." He says and the taod sage nods before he disappears in a puff of smoke.

Tsunade gets up and was about to speak up. 'Hold on Tsunade. I need to speak with you for a moment." He says and she turns to blink at him. "What is it sensei? I need to go check up on Shizune and Tonton." She says.

"I know but this won't take long. It's about Naruto." He says.

"What about him?" She asks.

"I know you just got back to the village but I was wondering… since the boy is in some form your last living relative, would you consider adopting him into your clan?" He asks and Tsunade's eyes widen.

"A-are you serious? Why would you ask me of all people to adopt him?" She asks and gets a smile from the old man.

"Tsunade… know you still hold some form of resentment with Konoha due to the death of your brother and your fiance." He says and her eyes widen slightly and turned around fully.

"But you shouldn't spend your life wallowing in self pity. You did the best you could to save Dan and you lost Nawaki due to the war, but they along with your grandfather and uncle wouldn't want you to live this way. If you adopt Naruto then you would have someone aside from Shizune in your life to live for." Tsunade looks away for a while but then speaks up.

"But why me? I don't think I'd be a good role model and influence for the boy." She states and Sarutobi shakes his head. "Don't doubt yourself Tsunade. You did manage to take care of Dan's niece since you left the village." He commented and Tsunade smiled sheepishly while rubbing the back of her head.

"More like she was taking care of me sensei." She said and he chuckled. Shizune was in a hotel sleeping on a bed and she sneezed. "All kidding aside Tsunade, I would like you to adopt him." He says and she thinks about it.

"What about the council?" She asks and the old man scoffs. "I have no issues with the shinobi council and clan heads but it's the civilians that'll be a pain, but I'll put those fools in their place. I may be old but I can still keep their sorry asses in line." He says with a dark grin on his face.

Tsunade has a smirk on her face. "I haven't seen that smile in a while. You're gonna screw them over aren't you?" She asks and the man nods keeping the smile on his face.

"I sure am and I'll show those fools what happens when you cross paths with the Shinobi no Kami." He answers. She ponders on the thought of adopting the kid.

She always wanted a kid after the second war ended with Dan and wanted to be a mother. But biologically he is related to her and there was no way she was gonna let Jiraiya adopt him and turn him into a pervert. "Okay sensei I've decided to adopt him since he is in a way 'related' to me and carries the DNA of a Senju and since I am part Uzumaki through my grandmother's side of the family." She says and he smiles.

"Thank you Tsunade. So do you plan on staying in Konoha? You can still leave whenever you want but you have to cut back on the sake and gambling." He says and she pouts.

"Fine." She relented while he snickers at how she was acting.

"One more thing Tsunade, make sure no one knows of Madara's DNA being implanted into Naruto. If Fugaku learns that Naruto could inheriting the Sharingan he'll stop at nothing to get him."

"I understand Sensai" Tsunade says and he sighs.

"Kami being the Hokage sucks." He mutters and she laughs and pats him on the back. That was when a nurse walked in.

"Hokage-sama, Tsunade-sama, the boy has awakened." She says. "Well let's go Tsunade." Hiruzen said to his student and they head to Naruto's room. Said blonde was opening his eyes slowly and looks up at the ceiling.

"Where am I? This isn't one eyes lab." He mutters and hears a voice in his head.

"**It's about time you woke up kit." **Said a deep yet melodic voice.

"Kurami-chan? Where the heck are we?" He asks. Kurami is the Kyubi and it was thanks to her that Naruto was still alive but at a price. She had to force half of her power into the seal and reverse the effect, turning Naruto into a hanyou. Naruto's speed, strength, stamina, senses, and healing factor increased to super human levels.

"**We're in the hospital. Apparently the Sandaime and his ANBU rescued you from that war hawk's clutches." **She says and he slowly sits up. His blue eyes were slitted he had a tint of red around the pupil. He sees the door open and Hiruzen and a blonde haired woman walk in.

"Hey Saru-oji, long time no see." Naruto says and the man smiles.

"Hey Naruto. How do you feel?" He asks

"Like my head is gonna split open." He answered before Tsunade walked forward.

"You seem to be suffering from a bit of head trauma. Here let me help." Tsunade offers and he looks at her and back at Sarutobi who nods.

"It's alright Naruto she's my student and the best medics in Konoha." He assured his surrogate grandson. Naruto nods and watches as Tsunade's hands glow green and she presses her hands against the sides of his head.

Naruto lets out a sigh of relief. "Is that better?" She asks and Naruto nods.

"Yes. Thanks pretty lady." He says with a grin on her face and she ruffles his head while eye smiling. "Well aren't you sweet?" She says and Hiruzen chuckles at this.

"Naruto I need to talk to you about your 'condition'." He says. "You mean the Kyubi?" He asks and their eyes widen in shock. "I found out from that Danzo guy and met her when I was 5. That guy did something to me that could've killed me but Kurami-chan kept me alive." He answers and Sarutobi's jaw dropped.

The Kyubi was female and she kept him alive all this time. "I see. Now Naruto I need to know has any part of your body felt… odd in some way like your eyes for example?" He asks and Naruto nods.

"Yeah my eyes kept feeling funny and when I open them, my vision is clearer and I can see an odd energy, I think it's called chakra and everything else seemed to move slower." He says.

Sarutobi's eyes widen. _'It must've been the Sharingan. I wonder.' _"Naruto can you try to focus chakra into your eyes?" He asks. Naruto nods and he focuses some chakra into his eyes. They were now crimson and there were three tomoe in each eye. Then the impossible happened, the three tomoe formed a ring as a three prong pinwheel formed in the center. (Madara's and Itachi's sharingan fused together)

"Can you see my chakra Naruto?" He asks and the blonde nods. "Apparently Naruto you have activated the Sharingan. It's a doujutsu that belongs to the Uchiha clan." He explains and Naruto looks at him.

"Oh. So does that mean that I'm an Uchiha?" He asks.

"More or less but they're not the only ones you're related to." He says and Naruto blinks in confusion. So for the next 10 minutes, Sarutobi explains to Naruto how Danzo injected the DNA of the two strongest Shinobi that ever lived in Konoha and a few from a different nation into his body. Naruto was shocked but was calm about it. Though the Sharingan Naruto had confused the old Kage and told himself he'd find the answers to it later.

"I see. So what's gonna happen to me?" He asks as he deactivates the Sharingan and Hiruzen smirks at him.

"Well Naruto Tsunade here is gonna adopt you since you are both related from your mother's side of the family." He says. Naruto's eyes were now the size of dinner plates.

"R-really?" He asks and Sarutobi nods.

"Yes really. Do you know the basics of being a shinobi?" He asks and Naruto nods.

"Yeah, that Danzo guy had some guys wearing blank masks teach me the basics but that's about it." He answered and Tsunade's finger twitched and Sarutobi frowned.

"I see. Naruto when they were 'training you did you go through any processes that would 'kill' your emotions?" He asks and Naruto blinked for a while and speaks up.

"Yeah he tried by having those guys with the blank masks cast something called genjutsu on me but thanks to Kurami-chan all they did was annoy me but she me told to play the fool and make them think they were 'killing' my emotions." He answered and their eyes widen at that.

"That's very impressive for someone your age Naruto. I'm sorry you had to go through that traumatic experience but don't worry. You won't have to worry about that fool ever again."

He says with a look of assurance on his face. Naruto looks at him smiles. "Thanks for getting me out of that place."

"You're welcome. Now then I'll be going to get the adoption papers ready for you and your new guardian Naruto." He says and then leaves the room. Tsunade sits in a chair and looks back at the blonde boy.

"Since I'm gonna be adopted by you do I call you Kaa-san, or Oba-san?" He asks. A smirk forms on her lips and she ruffles his hair again.

"I prefer to be called Kaa-san. Oba-san makes me sound old." She says while he grins at her.

"Okay… kaa-san. Are you gonna help tains to be a super ninja?" He asks.

Tsunade ponders on it for a while and nods. "Yes I'll be training you along with my assistant, Shizune." She says.

"Thanks. Are you really strong Kaa-san?" He asks and she chuckles and nods. "Yes I am… sochi. I am the strongest female ninja in the elemental nations. I can break a boulder with my index finger and cause earthquakes with a tap of my heel." She says and his eyes were the size of dinner plates when he heard that.

"Whoa! You can actually do that?" He asks and she nods.

"Do you think I can learn I can learn how to do that Kaa-san?" He asks with stars in his eyes.

"Sure. Once you get the basics of medical jutsu down I'll teach you how to do that." She says.

"Yes!" Naruto cries out and she laughs at this but in her mind she was wondering how Sarutobi and Jiraiya would react if they found out about her teaching Naruto the secret to her secret strength. Jiraiya was currently in Danzo's compounds looking for journals and files but then sneezes.

"Someone's talking about me. But why do I have this feeling in my body that I'm gonna suffer in the future and that Tsunade is the reason for it?" He mumbles while pulling out another journal.

Sarutobi also sneezed and felt a shiver go up his spine. "Something bad is gonna happen to me in the future and I believe that Tsunade and Jiraiya will be the cause of it." He says and finishes getting the adoption papers ready.

**Danzo's compound**

Jiraiya was currently reading a journal that had the title 'Project Chimera'. Apparently, this journal contained info on the previous failed experiment with former subjects that were kidnaped from various clans of Konoha.

"Just what the hell was Danzo thinking when he injected the boy with the DNA of the world's strongest ninja?" He says to himself as he closes the book and opens up a black file and on it had the names of said ninja.

As he reads off the names to himself he closes the folder and looks in a chest that contained several scrolls. His eyes widen when he sees one of the scrolls was a summoning that disappeared when Uzushiogakure was destroyed. "How the hell did that old bastard get his hands on these? I've got to report back to Sensei." He mutters and grabs the rest of the journals and shunshins out of the compound to inform the man about his recent discovery.

* * *

**OK everyone ADA with another story here. I know I know why am I doing another story…because I want to. I read Namikae09 Ultimate Shinobi and wanted to do one myself so I asked for his permission to do this.**

**Here's a list of Naruto's ability's.**

**Mokuton**

**Rinnegan**

**Eternal Mangekyo Sharingan**

**Magnet Release**

**Hozuki clan water abilities**

**Dust Release and Flight.**

**Now its time for a big long overdue rant.**

**WHAT THE HELL KISHIMOTO OR SHOULD I SAY STUPIDMOTO! I GOT TWO THINGS TO COMPLAIN ABOUT! First Madara, WTF! Now that the Uchiha severed his connection to Kabuto's summons he's basically it immortal now. No matter what happens he's always gonna heal from any and I mean ANY type of injure so I have no idea how the idiot plans on having him defeated. If Madara Uchiha had been alive when he fought the Kage he would of definitely have been killed but NO STUPIDMOTO had him basically kill them. FOR GODS SAKE Tsunade is bisected in half and even if she heals the kage and herself I can tell you right now she will definitely die.**

**Another thing is the Rinnegan. How dare STUPIDMOTO put that Nagato's Rinnegan was never his. That IT belonged to Madara the entire time. That is complete and utter bullshit. Here is what we the writers should do. Madara awaken his Rinnegan because he is a decedent of the Uchiha Clan Ancestor and Nagato awaken his Rinnegan because he is a decedent of the Senju clan Ancestor. FUCK YOU KISHIMOTO! **


	2. Chapter 2

Sarutobi was currently talking to Ibiki about what info he got out of Danzo and Jiraiya was there telling him about the files he found in the war hawk's office and the Professor was not happy in the least. He found out that Danzo kidnapped orphans and children from various clans within not only Konoha but other villages as well and trained them to be his army of emotionless drones loyal only to him. Funds from the village's treasury had been taken out by members of the civilian council to keep his ROOT Organization running after it 'disbanded' while they covered the missing funds up but that wasn't the worst of it. Danzo had his most trusted members infiltrate village of both major and minor countries to spy on them and to assassinate shinobi he deemed as a threat to Konoha. The worst was the massacre of the Prajñā Group of **Hayashi no Kuni **(land of Woods). Didn't that old war-hawk know he could have started another great war because of these missions.

He swore that Danzo would pay dearly for his crimes. He was still in his thoughts until he heard Jiraiya speak up. "Hey sensei, I also found a scroll that was from Ame. Apparently Hanzo made some sort of deal with Danzo to help him overthrow you if he had his drones assist them in dealing with the rebel forces." He explained and he handed it to the man.

Sarutobi looked at the scroll and growled dangerously. "And that was not the only thing I found. It would appear that Danzo took several scrolls from Kiri, Iwa, and Suna related to the abilities Naruto may possess." Jiraiya said as he produced several scrolls of the Hozuki clan's water abilities, the Tsuchikage's flight technique and Jinton, and the Kazekage's Jiton. "But that's not the worse Sensei. Two years ago Danzo abducted an entire Uchiha family and forced the brothers to butcher their parents and sister, which awaken their Mangekyo Sharingan which is the next stage of the Sharingan. Afterward he killed the brothers and implanted both their eyes into Naruto whiched unlocked the Sharingan's final form, The Eternal Mangekyo Sharingan." Jiraiya said which disgusted the two men.

"There's also something else Sensei."

"And that would be?" Sarutobi asked his student. Jiraiya pulled out two large scrolls of his back and set them down. The first scroll caught their attention as it had the kanji for **Iron Sand **on it. "Is that…" "Hai Sensei. It seems Danzo collected a large amount of iron powder for Naruto's Jiton." The two men then looked as the second scroll and their eyes widened and mouths hung open. "Th-that's…" On the second scroll was the kanji for Leviathan on it.

"Hai Sensei, the Leviathan contract. Apparently the war hawk raided the ruins of Uzushiogakure and stole the Leviathan contract from the Clan Leader's grave." Everyone knew of the Uzumaki Leader's personal summon, the Leviathans. Ancient beasts with power to rival the Biju themselves.

Hiruzen was now in a state of shock and could do the only thing that came to his mind. He fainted which caused Jiraiya and Ibiki to sweat drop. "This day just keeps getting better and better." Ibiki said sarcastically while Jiraiya sighs and nods in agreement, pulling out a vile of smelling salts.

**With Naruto**

Naruto was currently sitting in the hospital bed rubbing a happy Tonton behind the ear and that was when Shizune walked in. Naruto met Shizune right after Tsunade told her the she'd be adopting Naruto into her family which worried the brunette at first but Tsunade gave her a look that told her to back off as her decision was final.

"Hey Shizune-nee-chan." Naruto says and she smiles back.

"Hey Naruto-kun." Shizune says. "How are you doing right now?"

"Fine, Tonton's been keeping me company." She said while the pig oinks in agreement while Naruto patted her on the head. "So when can I get out of the hospital?" He asked the brunette.

"You're being released today and Tsunade-sama had me come here to pick you up and take you to her clan compound." She said and then pulled out some clothes which consisted of a white short sleeved shirt with red flames on the sleeves and hem of the shirt with a leaf spiral along with a pair of dark blue shorts along with blue ninja sandals.

"Finally I can get out of this hospital." He said as he got off the bed while Shizune blinked in confusion a couple of times.

"What's wrong Naruto-kun? Don't you like hospitals?" The brunette asks the young blonde.

"There's nothing wrong with the hospital it's just that it has a strong scent of medicine and it's killing my nose." He said as his face scrunched up while Kurami giggles tirelessly.

"**Don't worry kit that's only temporary until your body can handle your enhancements (yawns) well I need to take a long rest. Turning you into a hanyo cost me a lot of chakra."** Kasumi said.

"_How long do you need?" _Naruto asked the vixen who yawned again.

"**Give or take, at least 3 to 4 months since I can recover the power I lost easily. So until then I'm gonna cut our link off." **She said and then closed her eyes and drifted off into la la land.

Shizune however giggles at this. "Oh that well that's what a hospital usually smells like Naruto-kun now go into the bathroom and get dressed so we can meet up with your new Kaa-san." She instructed getting a nod from the young hanyo who took the clothes to change in the bathroom. Afterwards, Shizune signed Naruto out of the hospital and they along with Tonton left the hospital.

They were quiet as they made their way through the village until Naruto spoke up. "So Shizune-nee-chan, will you be helping me when Kaa-san trains me?" He asked the black haired brunette who smiled back.

"I'm pretty sure I will be helping you out Naruto-kun thought it'll mostly be in the basics of the medical arts. Tsunade-sama will more than likely teach you the advanced ones once you've gotten the basics down." Shizune explained and got a nod from the blonde.

"Oh okay so what's she like nee-chan?" Naruto asked Shizune who pondered on his question for a second and spoke up.

"Well Naruto-kun, aside from being the grandniece and granddaughter of the Shodai and Nidaime Hokage, Tsunade-sama is one of the best medics in the entire nation. She can easily heal any damage done to the body that some would consider a lost cause and cure nearly any form of illness. That and she is feared for possessing the strength that can rival a biju's." She finished explaining.

"Wow. So she's practically the strongest female in the world right?" He asked Shizune who nodded.

"Yes she is though she does have her faults like her terrible skills in gambling and love for sake and money. She also is very short tempered so making her angry is one thing you don't want to do unless you're Jiraiya-sama." She said sheepishly while rubbing the back of her head. Naruto on the other hand blinks a couple of times.

"….she's really that bad?" Naruto asked Shizune who slowly nodded.

"Yes she is." She answered with a sigh while they made it to the Senju compound. The brunette opened the door and let Naruto and Tonton in the house. "Tsunade-sama we're here!" She called out in the compound. As they walked into the living room they saw medical books of different sizes sitting on the coffee table, floor, and on the couches and said female Senju was lying back on the couch snoring lightly with an open book covering her face.

The female brunette sighs and shakes her head at her teacher's antics and walks over to her she inhales air into her lungs and pauses for a few seconds before. "TSUNADE-SAMA WAKE UP THE DEBT COLLECTORS ARE COMING TO GET YOU!" She screamed which made the female Senju jump out of the couch and look around frantically.

"RUN FOR THE HILLS SHIZUNE BEFORE THEY FIND OUR…. Room?" she stopped and blinked in confusion as she looked around the house only to see Shizune and Naruto covering their hands with their mouths giggling while a tick mark appeared on the back of her head. "I hate it when you do that." She muttered in an irked tone and then looked at her adopted son with a smile on her face.

"So Kaa-san when do you think we'll start on my training?" Naruto asked in an excited tone getting a raised brow from the woman.

"You're really stoked on training aren't you kiddo?" She asked Naruto who nodded excitedly.

"I sure am. I want to learn everything I can and become a strong ninja like you, Kaa-san." He said happily. Tsunade couldn't help but smile at his enthusiasm as it reminded her of Minato, Kushina, and her little brother Nawaki.

"And you will Naru-chan I assure you but what do ya say for now we spend the day getting to know each other while Sarutobi gets things settled?" She suggested before getting a nod from the blonde.

**Council Chambers**

Hiruzen Sarutobi was garbed in his Hokage robes and hat with his hands interlocked together and waiting on the Shinobi Council to enter the chambers since he informed the clan heads of an emergency session. That was when the council doors opened and walking into the chambers were the head members of each clan. Hiashi Hyuuga, Tsume Inuzuka, Inoichi Yamanaka, Shibi Aburame, Fugaku Uchiha, Chouza Akimichi, and Shikaku Nara.

Hiashi has long dark brown hair and featureless white eyes like all members of his clan and normally wears very traditional, loose fitting robes with a cloak.

Tsume has an animalistic look and she has long spiky brown hair, vertical slit-like pupils, elongated canine teeth and nails. She also has the clan fang markings on her cheeks as well as markings over her eyes and a dark shade of purple lipstick and she wears the standard outfit of a Konoha shinobi.

Inoichi has long blond hair reaching into his back, which he wears spiky on top and ending in a long ponytail, blue-green eyes and strong facial features. Inoichi is wearing the standard flak jacket over a black outfit, complete with hand-guards, forehead protector and a sleeveless red coat.

Shibi, like all members of his clan, has his eyes obscured by dark glasses which feature a single tassel hanging down from one-side. He has very spiky short black hair and a moustache. He typically wears a high collared outfit, while carrying a gourd on his back that is used for holding more kikaichū. He also tends to keep his hands in his pockets a lot, another trait he and his son share.

Fugaku had short, black hair and onyx eyes (when the Sharingan is not activated), with visible creases below them made more pronounced whenever he adopted a stern look. He wore the standard flak jacket, along with a black shirt with the Konoha Military Police Force symbol on the shoulders, shin-guards and a black apron with white diamonds on the bottom.

Chōza has long red hair and has markings on his cheeks, with the latter being a common trait in the Akimichi clan. He wears a samurai like outfit which entails a black suit completed with armor that has the kanji for "food" (食, shoku) on it. He also wears a rope belt, hand guards, and instead of a forehead protector, wears a piece of cloth tied around his head.

Shikaku has two scars on the right side of his face which are probably his most noticeable feature. He has dark hair tied up into a spiky ponytail, dark eyes as well as a goatee. His ears are also pierced. Shikaku wore a meshed shirt underneath his flak jacket, a deer skin coat over that and hand guards.

They each took their seats around their leader who remained silent before opening his eyes and gazing at each of them before sitting up straight. "Now that everyone's here I am sure you're all wondering why I called a meeting this early in the morning correct?" he asked the Clan Heads who nodded.

"Yes Hokage-sama and we are curious about the instant lockdown from last night?" Inoichi asked the leader of the village.

"Ah yes the lockdown the reason for that is because a traitor has been caught in our midst and that man is none other than Danzo Shimura." He answered, resulting in the clan head's eyes widening at the statement. "He was found not only with his so called disbanded ROOT organization still intact but also for smuggling classified Intel to unknown sources and current enemies of the village. Not only that but also taking missions that could have started another great war…" He shut his eyes for a few minutes before opening back up with rage and disgust in them which made some of them recoil since if the Professor ever got pissed then your ass was grass, "Danzo apparently had kidnapped Naruto Uzumaki Namikaze and spent the last six years attempting to turn the boy into an emotionless weapon and forced him to go through various experiments that could've killed him."

That right there made the members eye's widened in shock and some with utter disgust no their faces. "That sick bastard." Tsume Inuzuka snarled out and wanted to literally tear Danzo to pieces for putting a child through such a horrific thing.

"Trust me Tsume-san, what he has done is beyond sickening," Hiruzen said. "Apparently Danzo has integrated the DNA of the Shodai Hokage, Nidaime Mizukage, Nidaime and Sandaime Tsuchikage, and the Sandaime and Yondaime Kazekage." Explained the aged Hokage while keeping the fact that Madara Uchiha's DNA and the EMS (Eternal Mangekyo Sharingan) was also in Naruto a secret since he knew Fugaku would want the boy and stop at nothing to get him.

"That poor kid, to have gone through so much just because that monster wanted to create the ultimate ninja… he's no better than Orochimaru if not worse." Tsume lamented as did her fellow colleagues.

However no one noticed the gleam in Fugaku's eyes As he thought of bring the boy to the Uchiha side.

"Indeed and that is why Danzo will be tried and then executed for his actions."

"And the boy? What's to become of him Hokage-sama? Surely if what you say is true then it is possible he could without a doubt become the strongest ninja to ever be produced in the village if not even greater than his parents or any other Kage for that matter." Inoichi stated getting nods of agreement from the others.

"I already have a plan for that Inoichi and later on I'd like you to run a psychological evaluation in his mindscape but only to ensure he is mentally ready and due to the _training _Danzo put him through." Said mind walker nodded in agreement since unlike physical pain, suffering from mental trauma was not only more life threatening, but it can also destroy a person's will as the psyche is what keeps the human body stronger like the physical aspects.

**Later on that day**

**ANBU T&I Department**

Hiruzen was making his way across the barely lit hallways of the ANBU headquarters with two fully equipped and battle ready ANBU flanking his left and right and were heading to one of the torture chambers. There, they saw Ibiki Morino and two interrogators who also wore black coats like he did. The scarred man stepped forward and bowed at his leader who nodded back. "Hokage-sama." He greeted and Hiruzen nodded back.

"How is our 'guest' doing Ibiki? I'm pretty sure you gave him your best form of treatment?" Hiruzen asked Ibiki and got a grin that would send a chill down any person's spine.

"But of course Hokage-sama. Anything less and I wouldn't be doing my job." Ibiki answered and got a chuckle from his leader. "The Old war hawk sang like a canary once I was finished with him and got a list on who's under his influence on the council." He said as he reached into his pocket and pulls out a list of the people, handing it to Hiruzen who skimmed through it. His eyes widened in shock and then narrowed dangerously.

"Thank you for this list. Have several ANBU find the list of these people who dare undermine my authority and perform treasonous acts against me and my village and ring them here and have them 'prepared to join Danzo on the chopping block." He ordered Ibiki who nodded.

Afterwards, Hiruzen and his two ANBU approached the door while one of the interrogators opened the door and the Hokage enters. As he and his escorts do, the door closes behind him. His ANBU stay behind while the man walks into the barely lit room.

As he does he comes across the figure of one Danzo Shimura who was strapped to a chair, bound in chakra absorbing cuffs and paralysis seals over his body. His right arm and eye were removed and from the dried up blood on the floor as well as the bruises, cuts, and rips in his clothes, the interrogators showed very little mercy on the man. He was apparently staring at the ground, already knowing that his former friend/rival for the title of Hokage was in the room.

"So in the end it all came down to this." Hiruzen said in a disappointed and cold manner. "You've done everything in your power to claim everything I along with my mentors and Minato have worked so hard to create, all of the back-alley dealings and treasonous actions by allying yourself with people who would love nothing more than to destroy the village many ninja have lied and died for so that the next generation can prosper and become stronger."

Danzo remained silent as the man talked. "All of these actions and for what? So that you can gain the title of Hokage in order to start your own accursed ambitions?"

"It would've been for the good of the village." Danzo answered quietly.

"Spare me the bullshit Danzo!" Hiruzen snarled through his teeth. "What you have done was _not _good for the village! Nothing you did brought anything good to help make our village stronger! This is the reason why Tobirama-sense didn't choose you for the title as he saw the dark nature that resided in you and foresaw what you would've done if he had chosen you!" He leaned forward into Danzo's face and the man looked up at him with his single brown eye. "You've robbed ninja of their emotions and turned them into mindless puppets to be used and tossed away when they served no other purpose. You experimented on a child, a _child _for kami sake and not just any child, the child of our Yondaime Hokage! On top of that you allied yourself with Orochimaru, a true monster of this village.

Danzo simply smiled at the man. "Better to ally myself with the devil than be brought under this illusion of _piece _you and these other fools seem to believe in." He retorted before getting backhanded across the face by Hiruzen's knuckles. Blood dripped from the man's lower lip and the God of Shinobi stared at him coldly.

"Nothing I say will get into your head. As far as I'm concern you're nothing but an extremist and a traitor who's going to be executed but don't fret, your friends will be joining you on the chopping block by dawn." He then turned his back and walked towards the door. Danzo watched as the door opened and the three figure exit out of the steel door that was closed shut.

**The next day**

**The Chopping Block, Dawn**

Danzo Shimura was on his knees with his head on a small wooden structure ready to be chopped off. Next to him were members of the civilian council, the Hokage's advisers Homura Mitokado and Koharu Utatne, and the head of the civilian council Kizashi Haruno.

Konoha Anbu had swarmed into the homes of all the known traitors during the night and brought them to the T&I where they confessed to their crimes. Now they would pay for them.

The clan heads, as well as the rest of the village were gathered around the block with some of the civilians murmuring to each other about what was going on.

"People of Konoha…" Sarutobi began. "Today we are here to witness the execution of these traitors to Konoha who have committed graves crimes against the village and its people for their own ambitions. As such they will be executed via beheading and made examples of to those in the future who would dare turn their back on Konoha. Do the traitors have anything to say before their sentence is carried out?" Sarutobi said as Koharu spoke.

"Hiruzen please understand. What we did was for the good of Konoha. You were ruining this village so we had to…" The old bat never finished her sentence as Sarutobi gave her a vicious backhand to the face while Homura stayed silent, know that they had been caught red handed.

"LET MY HUSBAND GO THIS INSTANT!" a screeching banshee voiced tore throughout the whole block as everyone covered their ears. Mebuki Haruno marched up to the chopping block, determined to free her husband since she thought the Hokage had no real power and the council ruled the village. However before she could even get close, Tsunade appeared before her and gave the woman a viscous punch to the face that sent her crashing into an alley where everyone just left her there.

After everyone regained their hearing, Sarutobi ordered the executioner to carry the sentence. One by One the heads of each traitor were chopped off. However when the executioner reached Danzo who was last, several kunai appeared in his back while several explosions rang throughout the block.

"ANBU!" Sarutobi yelled while he discared his Hogake robes and hat. Looking at the chopping block Sarutobi saw Danzo was gone. His shinobi instincts kicked in as he jumped out of the way of several birds made of ink with explosive tags attached to them as they detonated. When the smoke from the explosion cleared everyone saw Danzo and a ROOT Anbu perched on top of a large owl.

"You are a full Hiruzen to think that 'all' of my secrets were discovered. Rest assured old _friend_ I will return and remake Konoha and then the world in my own image." The traitor said as the ink owl flew off away from the village.

* * *

**And that is the second chapter. Ok so Danzo is still loose (g****asp) but don't worry he will die. On another note Next week is finals so I won't be working on anything for a few weeks cause of all the studying and testing. **

**Bye bye for now. ADA out.**


End file.
